interpro-database

Query InterPro for protein family, domain, and functional site annotations. Integrates Pfam, PANTHER, PRINTS, SMART, SUPERFAMILY, and 11 other member databases. Use for protein function prediction, domain architecture analysis, evolutionary classification, and GO term mapping.

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저장소: zja2004/BGI-CLI
최근 소스 활동: 2026년 3월 19일 08:17
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import requests

BASE_URL = "https://www.ebi.ac.uk/interpro/api"

def interpro_get(endpoint, params=None):
    url = f"{BASE_URL}/{endpoint}"
    headers = {"Accept": "application/json"}
    response = requests.get(url, params=params, headers=headers)
    response.raise_for_status()
    return response.json()

def get_protein_entries(uniprot_id):
    """Get all InterPro entries that match a UniProt protein."""
    data = interpro_get(f"protein/UniProt/{uniprot_id}/entry/InterPro/")
    return data

# Example: Human p53 (TP53)
result = get_protein_entries("P04637")
entries = result.get("results", [])

for entry in entries:
    meta = entry["metadata"]
    print(f"  {meta['accession']} ({meta['type']}): {meta['name']}")
    # e.g., IPR011615 (domain): p53, tetramerisation domain
    #       IPR010991 (domain): p53, DNA-binding domain
    #       IPR013872 (family): p53 family

def get_entry(interpro_id):
    """Fetch details for an InterPro entry."""
    return interpro_get(f"entry/InterPro/{interpro_id}/")

# Example: Get Pfam domain PF00397 (WW domain)
ww_entry = get_entry("IPR001202")
print(f"Name: {ww_entry['metadata']['name']}")
print(f"Type: {ww_entry['metadata']['type']}")

# Also supports member database IDs:
def get_pfam_entry(pfam_id):
    return interpro_get(f"entry/Pfam/{pfam_id}/")

pfam = get_pfam_entry("PF00397")

def get_proteins_for_entry(interpro_id, database="UniProt", page_size=25):
    """Get all proteins annotated with an InterPro entry."""
    params = {"page_size": page_size}
    data = interpro_get(f"entry/InterPro/{interpro_id}/protein/{database}/", params)
    return data

# Example: Find all human kinase-domain proteins
kinase_proteins = get_proteins_for_entry("IPR000719")  # Protein kinase domain
print(f"Total proteins: {kinase_proteins['count']}")

def get_domain_architecture(uniprot_id):
    """Get the complete domain architecture of a protein."""
    data = interpro_get(f"protein/UniProt/{uniprot_id}/")
    return data

# Example: Get full domain architecture for EGFR
egfr = get_domain_architecture("P00533")

# The response includes locations of all matching entries on the sequence
for entry in egfr.get("entries", []):
    for fragment in entry.get("entry_protein_locations", []):
        for loc in fragment.get("fragments", []):
            print(f"  {entry['accession']}: {loc['start']}-{loc['end']}")

def get_go_terms_for_protein(uniprot_id):
    """Get GO terms associated with a protein via InterPro."""
    data = interpro_get(f"protein/UniProt/{uniprot_id}/")

    # GO terms are embedded in the entry metadata
    go_terms = []
    for entry in data.get("entries", []):
        go = entry.get("metadata", {}).get("go_terms", [])
        go_terms.extend(go)

    # Deduplicate
    seen = set()
    unique_go = []
    for term in go_terms:
        if term["identifier"] not in seen:
            seen.add(term["identifier"])
            unique_go.append(term)

    return unique_go

# GO terms include:
# {"identifier": "GO:0004672", "name": "protein kinase activity", "category": {"code": "F", "name": "Molecular Function"}}

def batch_lookup_proteins(uniprot_ids, database="UniProt"):
    """Look up multiple proteins and collect their InterPro entries."""
    import time
    results = {}
    for uid in uniprot_ids:
        try:
            data = interpro_get(f"protein/{database}/{uid}/entry/InterPro/")
            entries = data.get("results", [])
            results[uid] = [
                {
                    "accession": e["metadata"]["accession"],
                    "name": e["metadata"]["name"],
                    "type": e["metadata"]["type"]
                }
                for e in entries
            ]
        except Exception as e:
            results[uid] = {"error": str(e)}
        time.sleep(0.3)  # Rate limiting
    return results

# Example
proteins = ["P04637", "P00533", "P38398", "Q9Y6I9"]
domain_info = batch_lookup_proteins(proteins)
for uid, entries in domain_info.items():
    print(f"\n{uid}:")
    for e in entries[:3]:
        print(f"  - {e['accession']} ({e['type']}): {e['name']}")

def search_entries(query, entry_type=None, taxonomy_id=None):
    """Search InterPro entries by text."""
    params = {"search": query, "page_size": 20}
    if entry_type:
        params["type"] = entry_type  # family, domain, homologous_superfamily, etc.

    endpoint = "entry/InterPro/"
    if taxonomy_id:
        endpoint = f"entry/InterPro/taxonomy/UniProt/{taxonomy_id}/"

    return interpro_get(endpoint, params)

# Search for kinase-related entries
kinase_entries = search_entries("kinase", entry_type="domain")

# After running InterProScan and getting a UniProt ID:
def characterize_protein(uniprot_id):
    """Complete characterization workflow."""

    # 1. Get all annotations
    entries = get_protein_entries(uniprot_id)

    # 2. Group by type
    by_type = {}
    for e in entries.get("results", []):
        t = e["metadata"]["type"]
        by_type.setdefault(t, []).append({
            "accession": e["metadata"]["accession"],
            "name": e["metadata"]["name"]
        })

    # 3. Get GO terms
    go_terms = get_go_terms_for_protein(uniprot_id)

    return {
        "families": by_type.get("family", []),
        "domains": by_type.get("domain", []),
        "superfamilies": by_type.get("homologous_superfamily", []),
        "go_terms": go_terms
    }

Endpoint	Description
`/protein/UniProt/{id}/`	Full annotation for a protein
`/protein/UniProt/{id}/entry/InterPro/`	InterPro entries for a protein
`/entry/InterPro/{id}/`	Details of an InterPro entry
`/entry/Pfam/{id}/`	Pfam entry details
`/entry/InterPro/{id}/protein/UniProt/`	Proteins with an entry
`/entry/InterPro/`	Search/list InterPro entries
`/taxonomy/UniProt/{tax_id}/`	Proteins from a taxon
`/structure/PDB/{pdb_id}/`	Structures mapped to InterPro

Database	Focus
Pfam	Protein domains (HMM profiles)
PANTHER	Protein families and subfamilies
PRINTS	Protein fingerprints
ProSitePatterns	Amino acid patterns
ProSiteProfiles	Protein profile patterns
SMART	Protein domain analysis
TIGRFAM	JCVI curated protein families
SUPERFAMILY	Structural classification
CDD	Conserved Domain Database (NCBI)
HAMAP	Microbial protein families
NCBIfam	NCBI curated TIGRFAMs
Gene3D	CATH structural classification
PIRSR	PIR site rules